Experimental parameters affecting quantitative PCR of Artemia franciscana: A model for a marine zooplanktonic target in natural plankton samples

Limnology and Oceanography: Methods

Volumn 8, Issue JULY, 2010, Pages 337-347

  Mackie, Joshua A ^a,b   Geller, Jonathan ^a,b  

^a MOSS LANDING MARINE LABORATORIES   (United States)

^b SAN JOSE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTEMIA; ARTEMIA FRANCISCANA; CLUPEIDAE;

EID: 77956623698     PISSN: 15415856     EISSN: 15415856     Source Type: Journal    
DOI: 10.4319/lom.2010.8.337     Document Type: Article

References (47)

1. Baxevanis, A. D., I. Kappas, and T. J. Abatzopoulos. 2006. Molecular phylogenetics and asexuality in the brine shrimp Artemia. Mol. Phylogenet. Evol. 40:724-738 [doi:10.1016/j.ympev.2006.04.010].
2. Bell, A. S., and L. C. Ranford-Cartwright. 2002. Real-time quantitative PCR in parasitology. Trends Parasitol. 18:337-342 [doi:10.1016/S1471-4922(02)02331-0].
3. Boström, K. H., L. Riemann, U. L. Zweifel, and A. Hagström. 2007. Nodularia sp. nifH gene transcripts in the Baltic Sea proper. J. Plankton Res. 29:391-399 [doi:10.1093/plankt/ fbm019].
4. Boström, K. H., K. Simu, A. Haagström, and L. Riemann. 2004. Optimization of DNA extraction for quantitative marine bacterioplankton community analysis. Limnol. Oceanogr. Methods. 2:365-373.
5. Bott, N. J., and others. 2010. Toward routine, DNA-based detection methods for marine pests. Biotechnol. Adv. [doi:10.1016/ j.biotechadv.2010.05.018]
6. Bowers, H. A., T. M. Trice, R. E. Magnien, D. M. Goshorn, B. Michael, E. F. Schaefer, P. A. Rublee, and D.W. Oldach. 2006. Detection of Pfiesteria spp. by PCR in surface sediments collected from Chesapeake Bay tributaries (Maryland). Harm. Algae. 5:342-351 [doi:10.1016/j.hal.2005.09.005].
7. Brinkman, N. E., R. A. Haugland, L. J. Wymer, M. Byappanahalli, R. L. Whitman, and S. J. Vesper. 2003. Evaluation of a rapid, quantitative realtime PCR method for enumeration of pathogenic Candida cells in water. Appl. Environ. Microbiol. 69:1775-1782 [doi:10.1128/AEM.69.3.1775-1782.2003].
8. Browne, R. A., and G. H. MacDonald. 1982. Biogeography of the brine shrimp Artemia: distribution of parthenogenetic and sexual populations. J. Biogeography 9:331-338 [doi:10.2307/2844719].
9. Bustin, S. A. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Med. Endocrinol. 25:169-193 [doi:10.1677/jme.0.0250169].
10. Clary, D. O., and D. R. Wolstenholme. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization and genetic code. J. Mol. Evol. 22:252-271 [doi:10.1007/BF02099755].
11. Coyne, K. J., and S. C. Cary. 2005. Molecular approaches to the investigation of viable dinoflagellate cysts in natural sediments from estuarine environments. J. Euk. Microbiol. 52:90-94 [doi:10.1111/j.1550-7408.2005.05202001.x].
12. Coyne, K. J., and others. 2005. Improved quantitative real-time PCR assays for enumeration of harmful algal samples in field samples using an exogenous DNA reference standard. Limnol. Oceanogr. Methods. 3:381-391.
13. Folmer, O., M. Black, W. Hoeh, R. Lutz, and R. Vrijenhoek. 1994. DNA primers for the amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3:294-299.
14. Galluzzi, L., A. Penna, E. Bertozzinni, M. Grazia Giacobbe, E. Garces, S. Prioli, and M. Magnano. 2005. Development of a qualitative PCR method for the Alexandrium spp. (Dinophyceae) detection in contaminated mussels (Mytilus galloprovincialis). Harm. Algae. 4:973-983 [doi:10.1016/j.hal.2005.01.004].
15. Ginzinger, D. G. 2002. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp. Hematol. 30:503-512 [doi:10.1016/S0301-472X(02)00806-8].
16. Heid, C. A., J. Stevens, K. Livak, and P. M. Williams. 1996. Real time quantitative PCR. Genome Res. 6:986-994 [doi:10.1101/gr.6.10.986].
17. Holland, P. M., R. D. Abramson, R.Watson, and D. H. Gelfand. 1991. Detection of specific polymerase chain reaction product by utilizing the 5'- 3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 88:7276-7280 [doi:10.1073/pnas.88.16.7276].
18. Hong, Y.-K., S.-D. Kim, M. Polne-Fuller, and A. Gibor. 1995. DNA extraction conditions from Porphyra perforata using LiCl. J. Appl. Phycol. 7:101-107 [doi:10.1007/BF00693055].
19. Koressaar, T., and M. Remm. 2007. Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289-1291 [doi:10.1093/bioinformatics/btm091].
20. Kreuzer, K.-A., A. Bohn, U. Lass, U. R. Peters, and C. A. Schmidt. 2000. Influence of DNA polymerases on quantitative PCR results using TaqManTM probe format in the LightCyclerTM instrument. Mol. Cell. Probes 14:57-60 [doi:10.1006/mcpr.1999.0284].
21. Kutyavin, I. V., and others. 3'-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 28:655-661 [doi:10.1093/nar/28.2.655].
22. Kyle, M., T. Watts, J. Schade, and J. J. Elser. 2003. A microfuorometric method for quantifying RNA and DNA in terrestrial insects. J. Insect Sci. 3:1.
23. Livak, K., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-D CT method. Methods Mol. Biol. 25:402-408.
24. Livak, K. J., J. A. Flood, J. Marmaro, W. Giusti, and K. Deetz. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4:357-362.
25. Marco, R., R. Garesse, J. Cruces, and J. Renart. 1991. Artemia molecular genetics, p. 1-19. In R. A. Browne, P. A. Sorgeloos, and C. N. A. Trotman [eds.], Artemia biology. CRC Press.
26. Omori, M. H., and W. M. Hamner. 1982. Patchy distribution of zooplankton: Behavior, population assessment and sampling problems. Mar. Biol. 72:193-200 [doi:10.1007/BF00396920].
27. Owczarzy, R., Y. You, B. G. Moreira, J. A. Manthey, L. Huang, M. A. Behlke, and J. A. Walder. 2004. Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry 43:3537-3554. [doi:10.1021/bi034621r].
28. Pan, M., A. J. A. McBeath, S. J. Hay, G. J. Pierce, and C. O. Cunningham. 2008. Real-time PCR assay for detection and relative quantification of Liocarcinus depurator larvae from plankton samples. Mar. Biol. 153:859-870 [doi:10.1007/s00227-007-0858-y].
29. Perez, M. L., J. R. Valverde, B. Batuecas, F. Amat, R. Marco, and R. Garesse. 1994. Speciation in the Artemia genus: mitochondrial DNA analysis of bisexual and parthenogenetic brine shrimps. J. Mol. Evol. 38:156-168 [doi:10.1007/BF00166162].
30. Pfaffl, M. W. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29 e45 [doi:10.1093/nar/29.9.e45].
31. Popels, L. C., S. C. Cary, D. A. Hutchins, R. Forbes, F. Pustizzi, C. J. Gobler, and K. J. Coyne. 2003. The use of quantitative polymerase chain reaction for the detection and enumeration of the harmful alga Aureococcus anaphagefferens in environmental samples along the United States East Coast. Limnol. Oceanogr. Methods 1:92-102.
32. Rasmussen, R. 2001. Quantification on the LightCycler, p. 21-34. In S. Meuer, C.Wittwer, and K. Nakagawara [eds.], Rapid cycle real-time PCR: methods and applications. Springer.
33. Roh, C., F. Villatte, B.-G. Kim, and R. Schmid. 2006. Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples Appl. Microbiol. Biotechnol. 134:97-112.
34. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386.
35. Saito, K., T. Drgon, J. A. F. Robledo, D. N. Krupatkina, and G. R. Vasta. 2002. Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR based detection assays targeted to the non-transcribed spacer. Appl. Environ. Microbiol. 68:5394-5407 [doi:10.1128/AEM.68.11.5394-5407.2002].
36. Simonelli, P., C. Troedsson, J. C. Nejstgaard, K. Zech, and J. B. Larsen. 2009. Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies. J. Plankton Res. 31:1465-1474 [doi:10.1093/plankt/fbp087].
37. Struck, T. H., G. Purschke, and K. M. Halanych. 2005. A scaleless scale worm: Molecular evidence for the phylogenetic placement of Pisione remota (Pisionidae, Annelida). Mar. Biol. Res. 1:243-253 [doi:10.1080/17451000500261951].
38. Thompson, J. R., and others. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313 [doi:10.1126/science.1106028].
39. Töbe, K., B. Meyer, and V. Fuentes. 2010. Detection of zooplankton items in the stomach and gut content of larval krill, Euphausia superba, using a molecular approach. Polar Biol. 33:407-414 [doi: 10.1007/s00300-009-0714-2].
40. Troedsson, C., P. Simonelli, V. Verena, J. C. Nejstgaard, and M. E. Frischer. 2009. Quantification of copepod gut content by differential length amplification quantitative PCR (dlaqPCR). Mar. Biol. 156:253-259 [doi:10.1007/s00227-008-1079-8].
41. Vadopalus, B., J. V. Bouma, C. R. Kackels, and C. S. Freidman. 2006. Application of real-time PCR for simultaneous identification and quantification of larval abalone. J. Exp. Mar. Biol. Ecol. 334:219-228 [doi:10.1016/j.jembe.2006.02.005].
42. Vallejo, C. G., M. López, P. Ochoa, M. Manzanares, and R. Garesse. 1996. Mitochondrial differentiation during the early development of the brine shrimp Artemia franciscana. Biochemical. J. 314:505-510.
43. Weekers, P. H., G. Murugan, J. R. Vanfleteren, D. Belk, and H. J. Dumont. 2002. Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences. Mol. Phylogenet. Evol. 25:535-544 [doi:10.1016/S1055-7903(02)00289-0].
44. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-3751.
45. Wintzingerode, F. V., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229 [doi:10.1111/j.1574-6976.1997.tb00351.x].
46. Wright, N. A., J. Suzuki, B. Vadopalas, and C. S. Friedman. 2009. Development and optimization of quantitative PCR assays to aid Ostrea lurida Carpenter 1864 restoration efforts. J. Shellfish Res. 28:33-41 [doi:10.2983/035.028.0108].
47. Zipper, H., H. Brunner, J. Bernhagen, and F. Vitzthum. 2004. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 32:e103 [doi:110.1093/nar/gnh1101].